HPC Crash Course
Fundamentals in Computing & init()
Manuel Holtgrewe
Berlin Institute of Health at Charité
Welcome
Course Overview
Aims, Scope, Non-Aims, Out-of-Scope
Course Overview
Welcome to the course! 👋
Introduction to High-Performance Computing (HPC)
Focus on biomedical and medical research applications
🔬 ⌨️ 🧬
Duration:
5 days
5 x 45 min
Instructor: Manuel Holtgrewe
Contact Information: manuel.holtgrewe@bih-charite.de
User Engagement
We are a large group today.
We will use PollEverywhere for
quizes for “Lernerfolgskontrolle”
questions and answers
Let’s try:
PollEv.com/manuelholtgrewe153
The Sheep Scale
Course Aims and Scope
Basic understanding of HPC
Some theory to understand issues occuring in practice
How to help yourself in case of troubleshooting
Install software (conda, apptainer/singularity)
Tips and sleight of hand for improved productivity
… and maybe
Connect “birds of a feather” to later share experience, e.g., on project organisation
Course Non-Aims and Out-of-Scope
Advanced OnDemand Portal usage
(Linux) command line basics
Programming basics
Scientific programming, e.g., machine learning, statistics, visualization, parameter fitting, polars, …
Bioinformatics (variant/gene expression/… analysis)
Networking issues with Charite or MDC/MAX
Advanced Snakemake usage, reproducibility, …
Course Outline
Fundamentals: Computing
Fundamentals: HPC
Software Installation Management
Slurm Workload Manager
Snakemake for Workflows